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. 2020 Dec 9;15(1):21.
doi: 10.1186/s40793-020-00368-5.

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

Dipti W Pitta  1 , Nagaraju Indugu  2 , John D Toth  2 , Joseph S Bender  2 , Linda D Baker  2 , Meagan L Hennessy  2 , Bonnie Vecchiarelli  2 , Helen Aceto  2 , Zhengxia Dou  2
Affiliations

The distribution of microbiomes and resistomes across farm environments in conventional and organic dairy herds in Pennsylvania

Dipti W Pitta et al. Environ Microbiome. .

Abstract

Background: Antimicrobial resistance is a serious concern. Although the widespread use of antimicrobials in livestock has exacerbated the emergence and dissemination of antimicrobial resistance genes (ARG) in farm environments, little is known about whether antimicrobial use affects distribution of ARG in livestock systems. This study compared the distribution of microbiomes and resistomes (collections of ARG) across different farm sectors in dairy herds that differed in their use of antimicrobials. Feces from heifers, non-lactating, and lactating cows, manure storage, and soil from three conventional (antimicrobials used to treat cows) and three organic (no antimicrobials used for at least four years) farms in Pennsylvania were sampled. Samples were extracted for genomic DNA, processed, sequenced on the Illumina NextSeq platform, and analyzed for microbial community and resistome profiles using established procedures.

Results: Microbial communities and resistome profiles clustered by sample type across all farms. Overall, abundance and diversity of ARG in feces was significantly higher in conventional herds compared to organic herds. The ARG conferring resistance to betalactams, macrolide-lincosamide-streptogramin (MLS), and tetracyclines were significantly higher in fecal samples of dairy cows from conventional herds compared to organic herds. Regardless of farm type, all manure storage samples had greater diversity (albeit low abundance) of ARG conferring resistance to aminoglycosides, tetracyclines, MLS, multidrug resistance, and phenicol. All soil samples had lower abundance of ARG compared to feces, manure, and lagoon samples and were comprised of ARG conferring resistance to aminoglycosides, glycopeptides, and multi-drug resistance. The distribution of ARG is likely driven by the composition of microbiota in the respective sample types.

Conclusions: Antimicrobial use on farms significantly influenced specific groups of ARG in feces but not in manure storage or soil samples.

Keywords: Antimicrobial resistance; Dairy herd; Metagenomics; Resistome.

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Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
Community clustering patterns of microbiomes. Nonmetric multidimensional scaling (NMDS) ordination plot based on Euclidean distances calculated for each pair of samples and depicted by farm and sample types using the bacterial genus level information of metagenomic data. Ref: reference
Fig. 2
Fig. 2
Community clustering patterns of resistomes. Nonmetric multidimensional scaling (NMDS) ordination plot of resistomes of conventional and organic farms. Each of the four polygons represents a sample type. Ref: reference
Fig. 3
Fig. 3
Heat map of resistance mechanisms. Heat map showing resistance mechanisms for each class of antimicrobials identified in fecal, lagoon, manure, and soil sample types of conventional and organic farms. Relative abundance of each mechanism in each sample is given by the color code in upper right-hand corner of figure. Ref: reference; LactCow: lactating cow; NonLactCow: non-lactating cow
Fig. 4
Fig. 4
Bacterial hosts carrying ARG. Stacked bar plot depicting the percent contribution of bacterial hosts (identified to the phylum level) carrying ARG (antimicrobial resistance genes) for different classes of antimicrobials in each farm type
See this image and copyright information in PMC

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